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‎README.md‎

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<!-- lint disable -->
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**Documentation**
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**Code quality and style**
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**Unit tests and coverage**
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**How to cite**
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**Contributors**
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# CPP ROI
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## :warning: :warning: :warning:
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---
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## :warning:
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**This code is fairly unstable (:boom:) and might still change a lot.**
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**This code is fairly unstable and might still change.**
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Also this code currently has 0% test coverage...
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So make sure you "pin" which version or commit you are using for a given
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project, if you don't want your code to break in the future.
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---
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@@ -57,8 +48,7 @@ as a submodule, and intitialized when running `initCppSpm`.
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### Dependencies
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=======
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TODO
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======= TODO
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| Dependencies | Used version |
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| ---------------------------------------------------------- | ------------ |
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Also includes:
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- Yeo's 7 networks "atlas"
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- add REF and URL
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## Contributing
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## Contributors
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<!-- add REF and URL -->

‎demos/roi/step_7_get_ROI_PSC.m‎

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% This script will run through the ROIs made for each subject fo a ROI
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% based anaylisis using MarsBar to get a time course of the activations and
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% a percent signal change for each ROI and subject
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%
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% (C) Copyright 2020 CPP ROI developers
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clc;
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‎demos/roi/step_8_plot_PSC.m‎

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% This script will run through the ROIs made for each subject fo a ROI
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% based anaylisis using MarsBar to get a time course of the activations and
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% a percent signal change for each ROI and subject
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%
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% (C) Copyright 2020 CPP ROI developers
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% TODO
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% - refactor

‎initCppRoi.m‎

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@@ -12,20 +12,20 @@ function initCppRoi()
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pathSep = ':';
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if ~isunix
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pathSep = ';';
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pathSep = ';';
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end
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% we add all the subfunctions that are in the sub directories
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CPP_ROI_PATHS = genpath(fullfile(thisDirectory, 'src'));
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CPP_ROI_PATHS = cat(2, CPP_ROI_PATHS, pathSep, ...
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fullfile(thisDirectory, 'lib', 'marsbar-0.44'));
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fullfile(thisDirectory, 'lib', 'marsbar-0.44'));
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addpath(CPP_ROI_PATHS, '-begin');
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marsbar('on');
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try
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marsbar('splash');
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catch
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end
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CPP_ROI_INITIALIZED = true();
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else

‎src/atlas/returnAtlasDir.m‎

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%
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% (C) Copyright 2021 CPP ROI developers
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atlasDir = fullfile(fileparts(mfilename('fullpath')), '..', '..', 'atlas');
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atlasDir = fullfile(rootDir(), 'atlas');
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if nargin > 0
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‎src/roi/get_ROI_Coordinates.m‎

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function mni = get_ROI_Coordinates
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% This function gets the individual subject coordniates of the highest peak
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% within a specified Region of interest (usually coming from the group level univariate analysis)
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% Critical t-value for each experimental condition or mask file
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CriticalTs = 1; % Critical t-value for visual condition in L-V5 and R-V5 and bilateral PT
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%% load the data structure
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WD = pwd;
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%% group of subjects to analyze
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opt.groups = {'EB', 'SCa', 'SCv'}; % {'EB','SCa','SCv'};
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% suject to run in each group
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opt.subjects = {[1:13], [1:10], [1:6]}; % {[1:13],[1:10],[1:6]};
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%%
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smoothing = '6';
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%% Regions that will be used to extract the highest t-value within that mask
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maskFn = { 'face_lFFA.nii'
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'face_rFFA.nii'
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};
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CriticalTs = ones(1, length(maskFn)) * CriticalTs;
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%% Location of the data
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data_path = '/Volumes/SanDisk/Oli_Data/Categs_BIDS/derivatives';
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% create an mni cell with dimensions (1x number of masks)
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mni = cell(1, length(maskFn));
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SubNames = {};
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% for each mask
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for iMask = 1:length(maskFn)
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fprintf('Running Mask %.0f \n\n', iMask);
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CriticalT = CriticalTs(iMask); % get the critical t
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subCounter = 0;
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for iGroup = 1:length(opt.groups)
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for iSub = 1:length(opt.subjects{iGroup})
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fprintf('Running Subject %.0f \n', iSub);
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SubName = ['sub-', opt.groups{iGroup}, ...
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sprintf('%02d', opt.subjects{iGroup}(iSub))];
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fprintf('%s \n', SubName);
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subCounter = subCounter + 1;
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SubNames{subCounter, iMask} = SubName(5:end);
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%% the first 4 masks are for the FACE condition, the other 4
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% are from the SCENE condition
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if iMask <= 2
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result_file = [data_path, '/', SubName, '/stats/ffx_visMotion/ffx_', smoothing, '/spmT_0013.nii']; % HUMAN > BIG_ENV
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else
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result_file = [data_path, '/', SubName, '/stats/ffx_audMotion/ffx_', smoothing, '/spmT_0014.nii']; % BIG_ENV > HUMAN
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end
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%%
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mask_path = fullfile(WD, 'Kanwisher_ROIs', maskFn{iMask});
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r = load_nii(result_file);
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m = load_nii(mask_path);
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r.img(~m.img) = nan;
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maxVal = max(r.img(:));
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maxVals(subCounter, iMask) = maxVal;
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if maxVal > CriticalT %|| maxVal < CriticalT
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% Get the location of the higest t-value in slice space
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voxel_idx = find(r.img == maxVal);
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disp(maxVal);
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[x, y, z] = ind2sub(size(r.img), voxel_idx);
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% convert space from slice number to mni
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mni{1, iMask}(subCounter, :) = cor2mni([x y z], mask_path);
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% mni{1,iMask}(iSub,1) = mni{1,iMask}(iSub,1)* -1; % If masks created from AFNI or FSL,
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% the x coordinate could be flipped (multiplied x -1). If this is the case, multiply x with -1.
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mni{1, iMask}(subCounter, :);
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else
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mni{1, iMask}(subCounter, 1:3) = nan;
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end
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end
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end
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end
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save('mni_coordinates.mat', 'mni', 'maskFn', 'opt', 'maxVals', 'SubNames');
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end
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%%% cor2mni
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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function mni = cor2mni(cor, nifti_image)
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% function mni = cor2mni(cor, T)
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% convert matrix coordinate to mni coordinate
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%
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% cor: an Nx3 matrix
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% T: (optional) rotation matrix
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% mni is the returned coordinate in mni space
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%
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% caution: if T is not given, the default T is
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% T = ...
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% [-4 0 0 84;...
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% 0 4 0 -116;...
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% 0 0 4 -56;...
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% 0 0 0 1];
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%
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% xu cui
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% 2004-8-18
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% last revised: 2005-04-30
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% if nargin == 1
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% T = ...
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% [-4 0 0 84;...
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% 0 4 0 -116;...
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% 0 0 4 -56;...
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% 0 0 0 1];
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% end
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V = spm_vol(nifti_image);
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T = V.mat;
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cor = round(cor);
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mni = T * [cor(:, 1) cor(:, 2) cor(:, 3) ones(size(cor, 1), 1)]';
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mni = mni';
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mni(:, 4) = [];
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end

‎run_tests.m‎ renamed to ‎tests/run_tests.m‎

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% (C) Copyright 2019 CPP ROI developers
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% Does not work due to some relative path of the data when testing
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warning('OFF');
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spm('defaults', 'fMRI');
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folderToCover = fullfile(pwd, 'src');
8-
testFolder = fullfile(pwd, 'tests');
9+
testFolder = fullfile(fileparts(mfilename('fullpath')));
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folderToCover = fullfile(testFolder, '..', 'src');
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1013
success = moxunit_runtests( ...
1114
testFolder, ...

‎tests/test_unit_returnAtlasDir.m‎

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initTestSuite;
99
end
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function test_returnAtlasDir_no_input()
12+
13+
atlasDir = returnAtlasDir();
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15+
assertEqual(atlasDir, baseAtlasDir());
16+
17+
end
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1119
function test_returnAtlasDir_default()
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1321
atlasDir = returnAtlasDir('neuromorphometric');
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3947
function baseDir = baseAtlasDir()
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41-
baseDir = spm_file(fullfile(fileparts(mfilename('fullpath')), '..', 'atlas'), 'cpath');
49+
baseDir = spm_file(fullfile(rootDir(), 'atlas'), 'cpath');
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end

‎tests/test_unzipAtlas.m‎

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function test_unzipAtlas_default()
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13+
cleanUp();
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1315
unzipAtlas('wang');
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1517
assertEqual(exist( ...
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fullfile(returnAtlasDir('wang'), 'subj_vol_all', 'space-MNI_hemi-lh_dseg.nii'), 'file'), ...
18+
fullfile(returnAtlasDir('wang'), ...
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'subj_vol_all', ...
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'space-MNI_hemi-lh_dseg.nii'), ...
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'file'), ...
1722
2);
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1924
cleanUp();
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2732
if isOctave()
2833
confirm_recursive_rmdir (true, 'local');
2934
end
30-
rmdir(returnAtlasDir('wang'), 's');
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try
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rmdir(returnAtlasDir('wang'), 's');
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catch
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end
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end

‎uninitCppRoi.m‎

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% (C) Copyright 2021 CPP ROI developers
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function uninitCppRoi()
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global CPP_ROI_INITIALIZED
6-
global CPP_ROI_PATHS
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8-
if isempty(CPP_ROI_INITIALIZED) || ~CPP_ROI_INITIALIZED
9-
fprintf('\n\nCPP_ROI not initialized\n\n');
10-
return
11-
12-
else
13-
marsbar('off');
14-
rmpath(CPP_ROI_PATHS);
15-
CPP_ROI_INITIALIZED = false;
16-
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end
18-
19-
end
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global CPP_ROI_INITIALIZED
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global CPP_ROI_PATHS
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8+
if isempty(CPP_ROI_INITIALIZED) || ~CPP_ROI_INITIALIZED
9+
fprintf('\n\nCPP_ROI not initialized\n\n');
10+
return
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else
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marsbar('off');
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rmpath(CPP_ROI_PATHS);
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CPP_ROI_INITIALIZED = false;
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end
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end

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